The effect of the core atom type of the M@Au12 nanocluster (M = Au, Ag, Pt, and Pd) on the normal (NR) and charge-transfer surface-enhanced Raman spectroscopy (CT-SERS) of the zwitterion form of l-cysteine (ZWCYS) adsorbed on two different sites (D1 and D2) of the nanocluster is investigated separately in the gas phase and water. Because SERS requires the calculation of the absorption spectrum, the effect of the core atom type on the absorption spectrum of M@Au12 and its complex with the ZWCYS has also been investigated. The vibrational bands that show the intensity enhancement in the CT-SERS of the ZWCYS interacting with the D1 site of M@Au12 nanocluster in water are O─C═O asymmetric stretching (M = Au and Ag), NH2 bending (M = Ag), S-H stretching (M = Ag, Pt, and Pd), CH2 bending (M = Pt), and CH2 symmetric stretching (M = Pt and Pd). The ZWCYS at the D2 site of the M@Au12 nanocluster in water exhibits intensity enhancement for O─C═O asymmetric stretching (M = Pt), NH3 wagging (M = Au), and S-H stretching (M = Pd). The intensity of the vibrational bands of ZWCYS does not increase for M = Ag but decreases for O─C═O asymmetric stretching, S-H stretching, CH2 symmetric stretching, CH2 asymmetric stretching, and especially NH2 symmetric stretching.